From 63509f789438cbbc471a43da273ab39c78c9c8a0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 12 Feb 2021 16:29:42 -0600
Subject: [PATCH] Try removing stage-as from getData
---
rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index a3da729..65b4565 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -240,7 +240,7 @@ process getData {
input:
path script_bdbagFetch
- path cookies, stageAs: "deriva-cookies.txt" from bdbag
+ path cookies from bdbag
path inputBag from inputBag_getData
output:
@@ -258,7 +258,7 @@ process getData {
# link deriva cookie for authentication
echo -e "LOG: linking deriva cookie" >> ${repRID}.getData.log
mkdir -p ~/.bdbag
- ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt
+ ln -sf `readlink -e cookies.txt` ~/.bdbag/deriva-cookies.txt
echo -e "LOG: linked" >> ${repRID}.getData.log
# get bag basename
--
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